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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.31

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by:

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2025-09-29, 21:23 MDT based on data in: /home/moji-lin/rna-seq-reanalysis/data/processed

General Statistics

Showing ¹⁸/₁₈ rows and ¹¹/₁₇ columns.

Sample Name	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert	Reads	Reads mapped	% Reads mapped	% Aligned	M Aligned	Library types	CFR	M Bias	% Aligned
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633857 \| trimmed_KO_SRR13633857	0.15%	5.6M	26.8M	98.3%	0.0%	0.3%	27.3M	0.0bp	32.9M	32.4M	98.6%						98.3%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633858 \| trimmed_KO_SRR13633858	0.15%	5.6M	26.7M	98.1%	0.0%	0.4%	27.2M	0.0bp	32.9M	32.4M	98.4%						98.1%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633859 \| trimmed_KO_SRR13633859	0.15%	5.5M	27.0M	98.4%	0.0%	0.4%	27.4M	0.0bp	32.9M	32.4M	98.7%						98.4%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633860 \| trimmed_KO_SRR13633860	0.15%	5.4M	26.9M	98.4%	0.0%	0.4%	27.4M	0.0bp	32.8M	32.4M	98.7%						98.4%
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633855 \| trimmed_WT_SRR13633855	0.14%	6.2M	27.0M	98.5%	0.0%	0.4%	27.4M	0.0bp	33.6M	33.2M	98.7%						98.5%
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633856 \| trimmed_WT_SRR13633856	0.15%	6.7M	27.0M	98.4%	0.0%	0.4%	27.4M	0.0bp	34.1M	33.7M	98.7%						98.4%
processed \| quant_results \| trimmed_KO_SRR13633857 \| trimmed_KO_SRR13633857															100.0%	0.5
processed \| quant_results \| trimmed_KO_SRR13633858 \| trimmed_KO_SRR13633858															100.0%	0.5
processed \| quant_results \| trimmed_KO_SRR13633859 \| trimmed_KO_SRR13633859															100.0%	0.5
processed \| quant_results \| trimmed_KO_SRR13633860 \| trimmed_KO_SRR13633860															100.0%	0.5
processed \| quant_results \| trimmed_WT_SRR13633855 \| trimmed_WT_SRR13633855															100.0%	0.5
processed \| quant_results \| trimmed_WT_SRR13633856 \| trimmed_WT_SRR13633856															100.0%	0.5
quant_results \| trimmed_KO_SRR13633857 \| aux_info \| trimmed_KO_SRR13633857												94.5%	25.8M	U
quant_results \| trimmed_KO_SRR13633858 \| aux_info \| trimmed_KO_SRR13633858												93.8%	25.6M	U
quant_results \| trimmed_KO_SRR13633859 \| aux_info \| trimmed_KO_SRR13633859												94.3%	25.8M	U
quant_results \| trimmed_KO_SRR13633860 \| aux_info \| trimmed_KO_SRR13633860												93.9%	25.7M	U
quant_results \| trimmed_WT_SRR13633855 \| aux_info \| trimmed_WT_SRR13633855												94.5%	25.9M	U
quant_results \| trimmed_WT_SRR13633856 \| aux_info \| trimmed_WT_SRR13633856												93.0%	25.5M	U

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`samtools_flagstat-flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat-mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`samtools_flagstat-mapped_passed_pct`
\|\|	Salmon	% Aligned	% Mapped reads	`salmon-percent_mapped`
\|\|	Salmon	M Aligned	Mapped reads (millions)	`salmon-num_mapped`	read_count
\|\|	Salmon	Library types	Library types	`salmon-library_types`
\|\|	Salmon	CFR	Compatible fragment ratio	`salmon-compatible_fragment_ratio`
\|\|	Salmon	M Bias	Strand mapping bias	`salmon-strand_mapping_bias`
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`bowtie_2_hisat2-overall_alignment_rate`

Samtools

Version:


                      
                        1.19.2

HTSlib:


                      
                        1.19

Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Created with MultiQC

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633857 \| trimmed_KO_SRR13633857	27.3M	0.0M	0.0M	0.0M	0.0M	0.1M	1338.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633858 \| trimmed_KO_SRR13633858	27.2M	0.0M	0.0M	0.0M	0.0M	0.1M	1332.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633859 \| trimmed_KO_SRR13633859	27.4M	0.0M	0.0M	0.0M	0.0M	0.1M	1344.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633860 \| trimmed_KO_SRR13633860	27.4M	0.0M	0.0M	0.0M	0.0M	0.1M	1342.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633855 \| trimmed_WT_SRR13633855	27.4M	0.0M	0.0M	0.0M	0.0M	0.1M	1347.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633856 \| trimmed_WT_SRR13633856	27.4M	0.0M	0.0M	0.0M	0.0M	0.1M	1344.6Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

Flagstat

This module parses the output from samtools flagstat

Created with MultiQC

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633857 \| trimmed_KO_SRR13633857	32.9M	32.9M	32.4M	5.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633858 \| trimmed_KO_SRR13633858	32.9M	32.9M	32.4M	5.6M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633859 \| trimmed_KO_SRR13633859	32.9M	32.9M	32.4M	5.5M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633860 \| trimmed_KO_SRR13633860	32.8M	32.8M	32.4M	5.4M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633855 \| trimmed_WT_SRR13633855	33.6M	33.6M	33.2M	6.2M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633856 \| trimmed_WT_SRR13633856	34.1M	34.1M	33.7M	6.7M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M	0.0M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-table_table

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly_paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with_itself_and_mate_mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with_mate_mapped_to_a_different_chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed`	read_count

Flagstat: Percentage of total

This module parses the output from samtools flagstat

Created with MultiQC

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633857 \| trimmed_KO_SRR13633857	100.0%	100.0%	98.6%	16.9%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633858 \| trimmed_KO_SRR13633858	100.0%	100.0%	98.4%	17.1%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633859 \| trimmed_KO_SRR13633859	100.0%	100.0%	98.7%	16.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
processed \| Bam_related_logs \| logs_trimmed_KO_SRR13633860 \| trimmed_KO_SRR13633860	100.0%	100.0%	98.7%	16.6%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633855 \| trimmed_WT_SRR13633855	100.0%	100.0%	98.7%	18.4%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
processed \| Bam_related_logs \| logs_trimmed_WT_SRR13633856 \| trimmed_WT_SRR13633856	100.0%	100.0%	98.7%	19.7%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-flagstat-pct-table_table

Sort	Column	Description	ID
\|\|	Total Reads	Total Reads	`flagstat_total_pct`
\|\|	Total Passed QC	Total Passed QC	`total_passed_pct`
\|\|	Mapped	Mapped	`mapped_passed_pct`
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed_pct`
\|\|	Duplicates	Duplicates	`duplicates_passed_pct`
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed_pct`
\|\|	Properly Paired	Properly Paired	`properly_paired_passed_pct`
\|\|	Self and mate mapped	Self and mate mapped	`with_itself_and_mate_mapped_passed_pct`
\|\|	Singletons	Singletons	`singletons_passed_pct`
\|\|	Mate mapped to diff chr	Mate mapped to diff chr	`with_mate_mapped_to_a_different_chr_passed_pct`
\|\|	Diff chr (mapQ >= 5)	Diff chr (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed_pct`

Salmon

Version:


                      
                        1.10.3

Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197

Created with MultiQC

Bowtie 2 / HiSAT2

Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

Single-end alignments

This plot shows the number of reads aligning to the reference in different ways.

There are 3 possible types of alignment:

SE mapped uniquely: Read has only one occurence in the reference genome.
SE multimapped: Read has multiple occurence.
SE not aligned: Read has no occurence.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
Salmon	Salmon	`1.10.3`
Samtools	HTSlib	`1.19`
	Samtools	`1.19.2`

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General Statistics

General Statistics: Columns

Samtools

Percent mapped Help

Alignment stats

Samtools: stats: Alignment Stats: Columns

Flagstat

Samtools: flagstat: read count: Columns

Flagstat: Percentage of total

Samtools: flagstat: percentage of total: Columns

Salmon

Bowtie 2 / HiSAT2

Single-end alignments Help

Software Versions

v1.31

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Percent mapped

Single-end alignments